The history of this congregation reflects the development of religious institutions for African Americans in Charleston. Its roots stem from a religious group of free blacks and slaves organized in 1791. In 1816, black members of Charleston's Methodist Episcopal church withdrew over disputed burial ground, and under the leadership of Morris Brown, formed a separate congregation. The church's 1400 members soon thereafter established themselves an African Methodist Episcopal church, a denomination formally established in 1816 in Philadelphia, Pennsylvania. Two years later, Brown and other ministers of the church were jailed for violating state and local laws which prohibited religious gatherings of slaves and free blacks independent of white supervision.
During the Vesey controversy, the AME church was burned. Worship services continued after the church was rebuilt until 1834 when all-black churches were outlawed. The congregation subsequently met in secret until 1865 when it was formally reorganized, and the name Emanuel was adopted. Today, Emanuel AME Church is one of more than 1400 historically significant buildings within the Charleston Old and Historic District.
On the evening of June 17, 2015, a man opened fire on a Bible study group inside the church. The shooting left six women and three men dead: Rev. Clementa Pinckney, Tywanza Sanders, Cynthia Hurd, Rev. Sharonda Coleman-Singleton, Myra Thompson, Ethel Lance, Rev. Daniel Simmons, Rev. DePayne Middleton-Doctor and Susie Jackson. All of the victims were African American. President Barack Obama delivered the eulogy for Rev. Clementa Pinckney, church pastor and South Carolina state senator. The shooting prompted the removal of the Confederate flag from the South Carolina State grounds.